F.B.I. Official Who Investigated Major Attacks for Decades Is Stepping Down

It was Sunday night, a day after a bombing hit Manhattan last year, and investigators did not know who was in the car that had left the suspect’s home in New Jersey and was headed east on the Belt Parkway in Brooklyn. And they did not know where the car was going.

Intercepting it before its destination — perhaps a safe house — risked robbing the F.B.I. of a crucial lead. Hanging back risked letting the car get into the maze of Kennedy Airport and then get away or, far worse, letting the occupants launch an attack.

In a command post not far from the bombing site in Chelsea, with radio traffic crackling and an F.B.I. agent narrating the pursuit, chiefs from an array of law enforcement agencies weighed their options. The final call belonged to an F.B.I. special agent in charge of the counterterrorism division in New York who had forged his career in turf battles overseas and emerged as an ambassador within government for the F.B.I. way.

The agent, Carlos T. Fernandez, ordered the car stopped. Five people, some of them relatives of the bombing suspect, were in the car and were questioned. The suspect was arrested the next day.

Officials describe the investigation into the Chelsea bombing as a template for how the F.B.I. and the New York Police Department have learned to temper big egos and manage chain-of-command quandaries. It was also the product, in part, of Mr. Fernandez’s two decades’ experience courting foreign dignitaries and swaying his counterparts in American law enforcement and intelligence agencies while he investigated attacks by Al Qaeda beginning in the late 1990s.

He will retire from the F.B.I. on Friday as leader of the New York Joint Terrorism Task Force, in what amounts to a one-man exodus of operational know-how. Only a small number of counterterrorism agents involved in early Qaeda cases remain at the bureau. The New York task force, composed of about 500 investigators from dozens of local and federal agencies, is the oldest and largest such unit and handles cases in Canada, Western Europe and Africa.

“He was able to build relationships and build trust,” said Ali Soufan, who, as lead investigator of the bombing of the naval guided-missile destroyer Cole in Yemen in 2000, supervised Mr. Fernandez. “I think he was able to do something many other F.B.I. bosses for the J.T.T.F. were not able to accomplish to the level he did.”

Mr. Fernandez, 50, investigated two decades of major attacks, from the bombings of United States Embassies in East Africa in 1998 to the Paris attacks in 2015.

And he passed an unofficial test that agents who know the challenges of working in underdeveloped countries often use to judge their bosses: Did they take much Cipro, the antibiotic often used to treat intestinal infections? “He took a lot of Cipro in his life,” Mr. Soufan said.

Mr. Fernandez started his career on cases impeded by the wall between the C.I.A. and F.B.I. and ends his tenure at the bureau with connections across government, among them to the former C.I.A. director John O. Brennan, whom he met regularly as a top F.B.I. official assigned to the intelligence agency.

In Afghanistan around 2004, a Marine colonel several times declined the help of Mr. Fernandez and a colleague, Jeffrey Ringel, in interrogating people. But a casual comment by Mr. Fernandez about a Marine vehicle nearby ignited a conversation about the two agents’ service in the Marines. Eventually the colonel invited them on missions.

Mr. Ringel and Mr. Fernandez mentored Marines on how, instead of rounding up military-age men, they could use evidence and careful questioning to tie a few people to an attack.

“What he learned from his early days in Yemen is you can’t do this alone, you have to work as a team,” Mr. Ringel said. “And that’s what he did.”

Turf battles in New York could also be treacherous. As leader of the local terrorism task force, Mr. Fernandez was charged with further tightening bonds once badly frayed by the Police Department’s expanding counterterrorism mission after Sept. 11.

He sent emails to police colleagues starting at 3 a.m. and sped up information-sharing, said John Miller, the Police Department’s deputy commissioner for intelligence and counterterrorism.

After the Chelsea bombing, Mr. Fernandez had F.B.I. technicians work alongside the city bomb squad, and the F.B.I.’s evidence team worked alongside the city’s crime-scene unit.

J. Peter Donald, a Police Department spokesman, said Mr. Fernandez had endeared himself to colleagues by working long hours with them.

“You can have all the memorandums of understanding in the world, and they really don’t mean anything if people don’t like you,” said Don Borelli, a former assistant special agent in charge of the international counterterrorism branch in New York.

Mr. Fernandez brought back senior agents for a lecture series to pass on institutional memory. He credits his approach to what he learned from Mr. Soufan; James K. Kallstrom, the former F.B.I. assistant director; and John P. O’Neill, who led major investigations into Osama bin Laden and was killed in the Sept. 11 attacks.

“I certainly didn’t want our people to repeat the same mistakes that were made in the past,” he said in an interview this week.

Mr. Fernandez, who recently became eligible to retire, said that though he would have liked to see the Chelsea bombing case through, he chose to take an attractive offer in the private sector. He will become chief security officer at the entertainment conglomerate Viacom.

Mr. Fernandez said the experience of his parents in Cuba before they fled around the time of the revolution colored his commitment to handling investigations in the courts. “Hearing about my family members just being unilaterally arrested by the government without due process certainly had an impact on me and wanting to join the bureau,” he said.

Mr. Soufan said Mr. Fernandez had an easy manner with sources and refused to let a mission keep him from helping someone. In Yemen, not long after the Sept. 11 attacks, the pair received word that an American child about 10 years old had been kidnapped and was in the country. With no other agents on the ground, they put aside the terrorism case they were working, recovered the child and found a judge to sign paperwork they needed to fly him out of the country.

That the judge’s chambers were on the same block as a Qaeda outpost, Mr. Soufan said, did not deter Mr. Fernandez.

A version of this article appears in print on , Section A, Page 23 of the New York edition with the headline: F.B.I. Official Who Led Counterterrorism Inquiries for Decades Steps Down. Order Reprints | Today’s Paper | Subscribe